Any large scale projects I've taken on; I bag it, tag it and take lots of pictures. Additionally, I write a "To Do" list on a white board, broken down by systems, and a prospective date to start. Adjust accordingly and OFTEN
This keeps you on task, and gives you a continual sense of accomplishment and the ability to compartmentalize the whole thing (smaller chunks) Keep you from getting overwhelmed, without skipping steps if you need to say Stop the body work because its too cold outside, you can recover your seats in the basement instead.
Heres a basic list. Keep it orderly, keep track of your expenses, your receipts and keep a journal with the car so you can write down your experience. "I hate XYZ Parts, this fender didnt fit at all, lost 2 weeks making it right. I love Auto Gear, they got the thing done and invited me to bring the car down to the Nationals" When you're done, you can relive the experience. I spent 5yrs refurbishing a car with my dad in my late teens and early 20s. it was a great gift, to have stories of my own to share about his car, along with his. We don't own hot rods, so much as we're their caretaker now. Its important to pass that stuff on to your kids or the new owner.